Freshwater species face greater threats than terrestrial ones; however, conservation efforts for freshwater species lag far behind those for terrestrial ecosystems. Traditionally, conservation planning is often implemented independently for terrestrial and freshwater realms, ignoring potential incidental conservation benefits and cobenefits across them.

We established datasets of terrestrial and freshwater species in the Three Parallel Rivers Region, predicted their distributions using Biomod2, applied Marxan Connect to identify priority conservation areas (PCAs) for each group and evaluated their incidental conservation benefits and cobenefits.

Terrestrial PCAs were concentrated in mountain valleys (e.g., Gaoligong and Cangshan Mountains), while freshwater PCAs were clustered along four major rivers and lakes. Despite low correlations in irreplaceability (r = 0.34–0.45, p <0.001) and limited spatial similarity (Jaccard = 0.35–0.43), both PCA types yielded incidental benefits and cobenefits. Each PCA protected ≥ 80% of species and 52% of area in its own realm, while incidentally covering ≥ 79% of species and 42% of area in the other. Notably, terrestrial PCAs protected more freshwater species, whereas freshwater PCAs covered larger area for terrestrial species. Importantly, the greatest cross-realm cobenefits were achieved by the TS–FS PCAs, which yielded the highest coverage for both terrestrial (88.35% and 62.02%) and freshwater species (81.71% and 56.77%) and exhibited a strong synergistic relationship (y = 0.24x^1.31, R² = 0.85), while featuring overlapping PCAs that protected the highest proportions of species (80.45–91.28%) and area (46.25–63.04%) across taxonomic groups.

Synthesis and applications. Single-realm planning can yield cross-realm cobenefits, demonstrating strong potential for integrated conservation strategies. Integrating these cobenefits into cross-realm planning is key to advancing the “30×30” biodiversity targets.

We collected species occurrence data from multiple public databases and field surveys, including the Global Biodiversity Information Facility (GBIF.org, 2023), IUCN Red List of Threatened Species (IUCN, 2024), Chinese Virtual Herbarium (https://www.cvh.ac.cn/), Botanical Information and Ecology Network (Maitner, 2022), Integrated Digitized Biocollections (http://www.idigbio.org/portal), National Specimen Information Infrastructure (http://nsii.org.cn/), FishBase (Froese and Pauly, 2023), Investigation and Conservation of Aquatic Biological Species Resources in the Lancang River (Liu et al., 2016a), and Nujiang River (Liu et al., 2016b), Fishes in the Jinsha Jiang River Basin (Zhang et al., 2019), and the Fishes of Yunnan, China, Parts 1 and 2 (Chu and Chen, 1989, 1990). We performed data quality control by spatial and temporal cleaning (removing records with missing, unreliable, duplicate coordinates, and dates before 1950). Species names were standardized by verifying them against the Catalogue of Life (http://www.catalogueoflife.org), consolidating all records under accepted names and removing incomplete identifications. We subsequently thinned the data within 1 km grid cells using SDMtoolbox 2.6 (Brown et al., 2017). The final dataset (1950–2023) included records with precise coordinates and accepted names.

We then categorized the species into terrestrial and freshwater taxonomic groups based on Chinese Aquatic Plants (Chen et al., 2012), Aquatic Plants of China (Wang et al., 2021), FishBase (Froese and Pauly, 2023), the List of National Protected Wild Animals in China (NFGA and MARAPRC, 2021a), and the Atlas of Freshwater Biota in China (Han and Shu, 1995).

Based on Dryad’s Guidance for species data, we round critically endangered or endangered species coordinates to 1 degree, vulnerable species to 0.1 degree, and near threatened species to 0.01 degree. For endemic and protected species in our study, those endemic to the Nujiang, Lancang, and Jinsha rivers are rounded to 1 degree (as critically endangered), Yunnan endemics to 0.1 degree (as vulnerable), China endemics to 0.01 degree (as near threatened), national first grade protected species to 0.1 degree (as vulnerable), and national second grade protected species to 0.01 degree (as near threatened). For the remaining species, the original coordinates are provided.

The threatened status, Endemic status, and Protected grade classifications are based on the following sources:

IUCN Red List of Threatened Species (IUCN, 2024)

List of National Key Protected Wild Animals in China (NFGA and MARAPRC, 2021a)

List of National Key Protected Wild Plants in China (NFGA and MARAPRC, 2021b)

Species Red List of Yunnan Province (Gao and Sun, 2017)

China Red List of Biodiversity—Higher Plants (2020) (MEEPRC and CAS et al., 2023a)

China Red List of Biodiversity—Vertebrates (MEEPRC and CAS et al., 2023b)

Fishes in the Jinsha Jiang River basin (Zhang et al., 2019)

Investigation and Conservation of Aquatic Biological Species Resources in the Lancang River (Liu et al., 2016a)

Investigation and Conservation of Aquatic Biological Species Resources in the Nujiang River (Liu et al., 2016b)