The Chao Valley is located on the northern coast of Peru. Chao is a valley formed by the basins of the Chorobal River (north) and the Huamanzaña River (south), which converge in the lowest section of the valley to form the Chao River. The Chao Valley watershed (also referred to as the Huamanzaña Basin) covers an area of 1,429.00 km², with a length of 76.11 km and an average width of 18 km. The geology of the valley is characterized by fluvial and aeolian deposits, clasts, gravels, and clays. The hills that define the middle and lower valley consist primarily of andesite and rhyolite formations, with elevations below 550 m above sea level and an average gradient of 5% (Medina et al., 2012).

To examine the case of the lower Chao Valley, we gathered information from archaeological surveys previously conducted in the area. Among these, two surveys proved particularly relevant due to the number of sites recorded. The first was carried out in 1976 under the direction of archaeologist Mercedes Cárdenas (Milla and Cárdenas, 1996). Later, in 1988, another survey was led by archaeologist Santiago Uceda (Uceda, 1988; Uceda et al., 1990) in response to the development of the CHAVIMOCHIC inter-valley irrigation project—which integrates the valleys of Chao, Virú, Moche, and Chicama through hydraulic infrastructure designed to support industrial agriculture. This information was complemented by data from the SIGDA platform regarding the location of all archaeological sites in the middle and lower sections of the valley. (Milla and Cárdenas 1996) reported 190 sites of varying nature, size, and chronology: 126 located in the valley and 64 in adjacent areas. These sites are distributed across different sections and landforms, including floodplains, alluvial terraces, alluvial fans, ravines, and hillsides. The chronology of these sites encompasses the Middle Preceramic to the Late Horizon (circa 4000 BCE−1500 CE). Uceda's survey (Uceda, 1988; Uceda et al., 1990) focused on the areas of the Chao and Santa Valleys that were inside the area of the CHAVIMOCHIC irrigation project (the upper part of the lower valley). Here Uceda identified 21 sites in the Chao Valley and 35 in adjacent areas. Therefore, we consider that (Milla and Cárdenas 1996) is the most complete site inventory of the Chao Valley. The current record in the SIGDA platform for the Chao district includes 46 sites formally recognized. There are 159 sites recorded as “refenciales”, 35 archaeological areas recorded as “registrado referencialmente”. It is not clear what the difference is between these two categories. Additionally, there are 8 sites in the process of formal recognition, 2 sites with provisional protection, 23 sites as “BID declarado” and 68 sections of the Qapaq Ñam road system (the Inca Road system). Although the SIGDA record includes more sites than previous works at the valley, some sites appear more than once because of the ways the Ministry of Culture records site (e.g., when sites are cut by a road or a modern construction every section of the site is recorded individually), also this record shows sites that no longer exist (Supplementary Figure 4). This difference between current and past records has to do with the criteria used to identify and record a site.

Historical aerial imagery of the lower Chao Valley was obtained from the archive of the Servicio Aerofotográfico Nacional (SAN), specifically from flights conducted in 1957 and 1961. These images were used to create georeferenced mosaics for comparative analysis with more recent Google Earth imagery and drone-based aerial photographs. The selected years were chosen because they represent decades of relatively low agricultural activity and limited urban expansion, offering a valuable baseline for assessing subsequent landscape transformations.

In addition, data were compiled on risk factors, natural hazards, and critical zones associated with El Niño events, as well as on the geomorphological and hydrological characteristics of the Chao Valley. This information was sourced from materials identified during Phase A of the proposed methodology.

Based on this data, two areas were selected for both remote and on-the-ground exploration in the lower valley, one on the northern margin and one on the southern margin (Figure 1). Area 1 (north) was chosen due to its high concentration of archaeological sites, its susceptibility to environmental hazards, and its location within a zone of intense contemporary human activity (including agriculture and residential development). In contrast, Area 2 (south) was selected because it also contains a significant number of archaeological sites, is situated within a geomorphologically distinct zone compared to Area 1 and is relatively isolated from modern settlements and activities. This selection strategy was intended to facilitate a more comprehensive assessment of the conditions affecting the lower Chao Valley.

Direct fieldwork in the selected areas was carried out in 2019 and 2021. In accordance with the objectives of this phase, the following activities were undertaken:

Chao's climate is warm and dry, with an annual average temperature ranging from 18° to 25 °C and a relative humidity of 78%. The Chorobal and Huamanzaña rivers have minimal water flow, typically between January and April; however, in regular years, the annual average discharge is approximately 0 m³/s (Autoridad Nacional del Agua, 2025; Supplementary Figure 5). In this arid environment of the northern Peruvian coast, precipitation associated with Eastern Pacific El Niño and Coastal El Niño events has a significant impact (Supplementary Figure 5), as these phenomena are linked to the main geological and hydrogeological hazards reported in the valley, including floods, landslides, debris flows, riverbank erosion, and sand deposition. According to studies conducted in the valley (Medina et al., 2012; Medina Allcca et al., 2017; Núñez Juárez et al., 2017), the main hazards identified in the middle and lower sections are related to the effects of El Niño (Figures 3, 5, and Tables 1, 3, 4). This pattern is consistent across most of the Peruvian coast, particularly along the northern and central regions, where the effects of El Niño are most intense. For this reason, El Niño represents the primary natural risk factor for the conservation of archaeological sites in the Chao Valley. However, although sociocultural factors are not the focus of this article, it is important to emphasize that, at present, human activity has the most frequent and severe impact on archaeological sites in Peru (Tapullima and Ortiz, 2018).

The application of this methodology in the Chao Valley has allowed us to corroborate several initially proposed aspects and assess the scope and resolution of the collected data. First, while the SIGDA platform inventory constitutes an official national registry, it remains an ongoing inventory that must be supplemented with additional information from other local registries and photographic archives. Moreover, this platform contains outdated information, including sites that have already disappeared under areas where modern constructions have been built over former archaeological zones or agricultural fields occupy the former archaeological areas (Supplementary Figure 4). Therefore, combining cadastral data is the most effective approach to obtaining an up-to-date inventory of archaeological sites. Additionally, geological and geomorphological information available through platforms such as GEOCATMIN proved highly useful for identifying hazards in the area. However, due to the scale of the available data (1:50,000, 1:100,000), certain aspects require further refinement. For instance, during the exploration of the southern margin of the lower valley, we identified the presence of alluvial plains and fans in areas previously reported as “sand mantles” (Supplementary Figure 4). These details should be refined through direct field exploration of the selected monitoring areas.

Furthermore, the analysis of the collected data reveals a widespread distribution of archaeological sites in the lower Chao Valley (Table 1), most of which are located at elevations below 250 m above sea level (Figure 2), on alluvial plains and terraces (Figure 5). Consequently, elevation- and slope-related hazards, such as mass movements and landslides, are not significant in this valley (Figure 4). In the lower valley, most of the sites recorded in this study are situated in areas of high and moderate susceptibility to fluvial flooding (Figures 3, 5). Therefore, the most critical hazards in the lower Chao Valley include flooding, debris flows, and aeolian deposition (Table 3), all of which are linked to anomalous precipitation events on the Peruvian coast—namely, the occurrence of El Niño. These areas are also associated with agricultural fields and population centers (Supplementary Figure 2). As a result, archaeological sites are affected by the deposition of alluvial sediments, structural collapses, sand accumulation, and intentional destruction due to modern activities.

Excavations at the site of Las Salinas de Chao (Exploration Area 2) revealed a strong correlation between the information gathered during Phases A and B concerning the archaeology, geology, and geomorphology of the area. Las Salinas de Chao is a monumental site covering 21.5 ha, featuring stone-built structures distributed along the slopes of the Coscomba hills and the adjacent alluvial plain. Our excavations revealed the presence of alluvial deposits within the plain, consisting primarily of gravel and coarse sand deposited during various occupational phases of the site, and in some sectors, after its abandonment. Although the alluvial plain also exhibits the presence of aeolian deposits, their extent is more limited and does not appear to have caused significant damage to the archaeological structures.

The areas at the base of the hillsides and on the hillsides themselves presented evidence of sediment flows and displaced stone blocks originating from higher elevations—transported downslope via minor ravines—both during the site's occupation and after its abandonment (Supplementary Figure 6). Data collected during Phase A suggested the presence of extensive sand mantles over archaeological areas; however, our field observations indicate that the actual extent of these deposits is somewhat smaller, primarily affecting sectors closer to the coastline.

When we compare the sites recorded in 1976 with the current register of archaeological sites recognized by the Ministry of Culture in the SIGDA platform, a significant loss of sites becomes evident, particularly in the lower valley on both banks of the river (Supplementary Figure 7). In 1976, 33 sites were documented in Exploration Area 1 alone; by 2025, this same sector contains 15 sites (Supplementary Figure 7), representing a 54% loss.

Within Exploration Area 2, the most frequently recorded and impactful threats to the preservation of archaeological sites were, in order of prevalence: sediment flow, mass movement, and sand encroachment.In contrast, in Exploration Area 1, the most frequently recorded and impactful threats to the conservation of archaeological sites are related to human activity, particularly agricultural practices. This is followed by flooding and fluvial erosion, which have affected archaeological sites through the deposition of fine sediments and the destabilization of alluvial terraces caused by erosion processes. Lastly, sand encroachment impacts areas located closest to the coastline.

Overall, the state of conservation of archaeological sites is notably better in Area 2, primarily due to the limited presence of human activity (restricted mainly to poultry farms), the absence of permanent settlements, and its location outside the river's floodplain. Both areas, however, remain susceptible to hazard events triggered by anomalous rainfall in the valley. These include flooding and fluvial erosion in Area 1, and debris flows and mass movement in Area 2.

Following the application of this methodology to the lower Chao valley, it was applied to the lower Cañete valley. Administratively, the Cañete River basin is located within the provinces of Cañete and Yauyos, both of which belong to the Lima Department. The Cañete River Valley, with 24,052 ha of cultivated land, lies in the south-central coastal region of Peru, at the southernmost point of the Lima Department. Physiographically, this area consists of the Cañete River's alluvial plain and the alluvial fans of Quilmaná and Conta (Rosas et al., 2020).

The Cañete River is part of the Pacific or Western watershed, spanning 220 km with an average slope of 2%, from its source at the Ticllacocha lagoon to its mouth in the Pacific Ocean. The basin consists of two areas: a mountainous zone that covers approximately 95% of the total area, and an alluvial zone (the Cañete River Valley) in the lower part, which covers the remaining 5%. This alluvial area has a nearly flat relief with a gentle slope, interrupted by hills and smaller elevations, covering an area of 310 km². The area has been divided into seven distinct landscapes based on the origin, genesis, and form of the material. These include the alluvial plain, alluvial fans, marine landscape, marine-alluvial landscape, aeolian action landscape, and witness hill landscape. Within the alluvial area lies the region known as the Valley, which contains the highest concentration of agricultural land in the basin, as well as archaeological sites.

The valley receives 200–300 mm of rainfall annually, classifying it as semi-desert. Most precipitation occurs during the rainy season from December to March, but the amount and distribution can vary significantly each year. The Cañete valley faces significant hydrogeological risks as it is highly susceptible to flooding, particularly during El Niño events, which can cause river overflow and landslides that impact agriculture and infrastructure (Instituto de Defensa Civil, 2002).

It is important to note that the Cañete valley presents one of the most fertile valleys in Perú. Since its river plain is wide, it presents ample flat land for agriculture, as well as water year-round. The irrigation system that waters the lower valley was constructed in pre-Hispanic times (Fernandini Parodi, 2018) and has been improved throughout the years. During colonial times, Cañete housed large haciendas, which became even larger latifundios during republican times. In 1969, President Velasco Alvarado changed the rural landscape of Perú by implementing an Agrarian Reform, which expropriated large latifundios from its owners and gave the land to the farmers, who in turn organized themselves into agrarian cooperatives. Agrarian cooperatives lasted until 1984, when the government started a parceling process going back to individual farmers (Portocarrero, 1987). All these changes had profound effects on the agricultural, and indirectly, cultural landscape.

In terms of archaeology, the lower Cañete presents a total of 225 recorded archaeological sites. The first surveys were performed by Carlos Williams and Manuel Merino between 1977 and 1978 who recorded 163 archaeological sites (Williams and Merino, 2006). The remaining 62 sites were recorded by Fernandini in 2022 (Fernandini, 2023). Most of these sites are located in what is today agricultural lands, although larger sites can be found on top of low hills. These archaeological sites date from the early Preceramic period (ca. 9000 BP) to the Late Horizon (1400–1532 CE), showing a continuous occupation throughout time.

We compiled data from previous surveys performed in the valley, mainly from Williams and Merino (2006), and from the Ministry of Culture inventory and SIGDA (which was based on the original Williams and Merino survey). Moreover, we obtained aerial photographs from the SAN archives. These photographs date to 1961 and 1966. These dates are important since between 1970 and 1984, the agricultural landscape experienced changes due to the Agrarian Reform. We also collected data on areas vulnerable to flooding and land mass movement from national institutions such as INGEMMET, INDECI and CENEPRED, which was analyzed in conjunction with a collection of GIS data and reports from the GEOCATMIN platform.

Following the collection of data, we made an initial identification of areas vulnerable to geological risks such as flooding and land mass movements, and also to urban and agricultural expansion. Based on this initial identification we selected areas for exploration in the lower valley and generated a series of exploration polygons for direct field assessment.

During the direct exploration phase, we performed on-foot and drone exploration of the selected areas. When access was allowed, we walked and recorded archaeological sites by foot, nevertheless some sites were within private property, mostly inside agricultural lots surrounded by high walls, these were recorded by drone.

We generated aerial photographic models of the selected polygons using the software Pix4Dcapture to create automated flight plans, using an overlap of 70% and at an altitude that did not exceed 150 m. In order to achieve accurate georeferencing we took control points using a Trimble GNSS.

Five archaeological sites that presented different geological characteristics were excavated for stratigraphic exploration. The sites selected were:

After collecting different sources of information both using digital and physical methods, we proceeded to process this information. We used QGIS to process this data in different layers in order to perform different types of spatial analysis. Our layers included: aerial photogrammetric models of the polygons selected, aerial photographs from 1961, a layer of archaeological sites which existed until 1961 which sums to sites and a layer of archaeological sites that exist in 2024, in total. Moreover, we also included GIS information obtained from the different national organizations such as INGEMMET and CENEPRED, that included the distribution of urban areas, geomorphologic, topographical and hydrogeological information, data regarding areas vulnerable to flooding, land mass movements, geological risk and the El Niño phenomenon. Using these different sources, we managed to obtain important information regarding site preservation in relation to risks linked to urban and agricultural growth and flooding.

In order to explore site preservation and its relation to natural and cultural phenomena, we first focused on making a comparison between site preservation in 1961 vs. 2024. Figure 6 shows a total of 255 archaeological sites. From these we have differentiated sites registered in 1961, recorded from aerial photographs, and sites registered in 2024, recorded from Google Earth, aerial photographs taken by the project and on foot inspection. From the 255 archaeological sites recorded in 1961, only 163 were recorded in 2024. That is 92 sites have been destroyed in the last 63 years, a 36% loss.

In order to explore the different factors affecting site preservation, we used information regarding agricultural expansion, population expansion and geological factors such as flooding or land mass movements. For instance, regarding agricultural expansion, we have used information of cultivated land in 1986 and 2019, when the last agrarian census was performed, as well as sites preserved until 1961 and 2024 (Figure 7). It is clear that most archaeological sites within the Cañete valley lie within agricultural land. Out of the 255 archaeological sites in the lower valley, 218 lie within current agricultural land. Visual inspection of the 1961 aerial photographs show that the valley was actively cultivated in those times, yet given the presence of several archaeological sites within agricultural land it seems farmers were avoiding archaeological sites and, to some extent, guaranteeing its preservation. This scenario changed drastically in 2024 when out of the 218 archaeological sites that existed in 1961 within agricultural land, only 138 were preserved, that is 80 archaeological sites had been destroyed. On closer inspection, we can observe that several of the non-preserved sites were destroyed between 1986 and 2024. This is an important date, since it was between 1984 and 1986 that cooperatives disintegrated to give way to the parceling of agricultural land. Out of the 92 sites destroyed by 2024, 28 were destroyed by agriculture expansion from 1986 onwards.

While agricultural expansion seems to be the main factor in site destruction between 1961 and 2024, we also explored the relation between populated areas and site preservation. Figure 8 shows information regarding sites preserved in 1961 and 2024, and its relationship with populated areas. This map shows there is a cluster of non-preserved sites that used to be located near the largest population cluster, that is the city of San Vicente, the capital of the Cañete province. On a lesser scale, we can observe that the second largest population cluster, San Luis de Cañete, is also linked with archaeological sites that are no longer preserved. This information shows there is a clear relationship between the urban growth of this city and the disappearance of archaeological sites. Out of the 37 archaeological sites located close or within currently populated areas in 1961, only 17 exist in 2024. Which shows a 56% decrease in site preservation.

Based on these maps we can observe the agricultural and population growth represents a serious factor in site preservation, particularly since 1961 onwards. On the other hand, hydrological risks associated with flooding and land mass movement are factors that also affected the preservation of sites in the long term. As we can see in Figure 9, the lower Cañete valley presents two basins, the Cañete River Basin (purple), and the Pocoto Basin (green). The latter is composed of a series of quebradas that gather water from the high and middle valley, affecting the central and northern portion of the lower valley, as is reflected in light-blue in the map, and marked as an area of high hydrological risk. Coincidentally the area marked as hydrological risk at the center of the valley lies on top of San Vicente. The map also shows the location of geological risks associated with land mass movement, mainly the falling of rocks associated with the activation of quebradas or earthquakes.

When examining the relationship between hydrological and geological risks and the distribution of archaeological sites, one area emerges as particularly significant: San Vicente (Figure 10). This zone not only hosts a high concentration of sites but is also classified as high-risk. As previously noted, several archaeological sites recorded in 1961 are no longer present in 2024. While this loss can partly be attributed to urban expansion, recurrent flooding likely played a significant role in their disappearance. Site distribution analysis in the lower valley (Table 1) reveals that the majority of sites (220) are located on alluvial plains, with only a small number situated on hillsides (4) or hilltops (4). A ground survey of the high-risk zone at the center of the valley shows that only hilltop sites have survived, suggesting that ground-level sites were either destroyed by flooding or that these areas were consciously avoided due to their vulnerability. Regarding geological risks, the lower valley contains few high-risk zones, with most geological hazards concentrated in the middle valley, where the terrain becomes narrower and steeper.

Finally, we have identified geological and hydrogeological processes in the Cañete valley (Table 3). For the lower Cañete valley, we can observe sand deposition mainly due to wind erosion and flooding. Processes such as mud and debris flow are also present linked to heavy rains in the high and middle valleys, which activate quebradas in the lower valley.