We describe the successful application of a 4-decade analysis of an Index of Biotic Integrity (IBI) demonstrating its assessment value when applied to the fish community of Lake Chapala. We based our analysis on fish community and fishery composition and on the proportion and density of native and exotic species for each decade. Fisheries landings and IBI values document a long-term downward trend since the 1970s. Data from the 1990s and 2000s reveal a dramatic drop in the IBI score to 20 points (out of a possible 100), a rating of very poor. The fisheries collapse and the loss of 11 native species as a consequence of habitat degradation and invasive species have reduced native fish biomass and richness. Fluctuations in rainfall, principally, and water-extraction related to human activities have had a major impact on the lake. Additionally, water quality deterioration has been caused by a lack of wastewater treatment. The fish community has been further modified by large increases in the number and biomass of exotic fishes. Although the exact degree of decline in biotic integrity is impossible to determine because of uncertainty about the representativeness and accuracy of some historical information, the analysis of the temporal changes in the IBI provides compelling evidence for an accelerating drop in ecosystem health. The application of IBI, which is broad in scope and has flexible data requirements, can serve as a template for assessing trends in other water bodies with a history of fisheries data but limited standardized monitoring of the fish community.

Subtropical rivers in developing countries often lack adequate monitoring, which makes it difficult to comprehensively determine their water quality when faced with different anthropic impacts. There are no proper protocols in the regulations to incorporate indicators and adapt them to different biogeographic regions, limiting the potential success of conservation and restoration of river ecosystems. This study proposes implementing macroinvertebrates as bioindicators of water quality in river ecosystems, and modifying the calibration of the widely used Biomonitoring Working Party (BMWP) index for its adaptation in a subtropical river. The Duero River, Mexico, was used as an example in this study. Data were explored with multivariate statistics, and the water quality and habitat values were averaged to obtain the families’ bioindication values and the index categories. The BMWP adequately described a deterioration gradient from the origin to the river mouth (from fair to extremely polluted), with some intermediate recovery points related to the presence of springs. Its performance was compared with other biological indices and exhibited a positive relationship with all of them. In addition, how BMWP changed over time was analyzed by examining previous samples, and highlighted increased river deterioration over time. A calibrated BMWP will allow for long-term monitoring at a low cost.