The intensive use of pesticides in Mexican agriculture has contributed significantly to the increase in food production, but at the same time represents potential risk to biota. This situation creates a dilemma between the need to increase food production and the preservation of the environment and human health. Aquatic invertebrates play a vital role in the balance of aquatic ecosystems but are sensitive to pesticides contamination. The sensitivity of aquatic invertebrates to pesticides contamination has led them to be used to assess the potential impact of this contamination on aquatic ecosystems. In the present study, conducted in the Ayuquila-Armeria basin, the following aims were achieved: 1) quantifying the presence of 20 pesticides in river sediments, 2) assessing the spatiotemporal distribution of pesticides in river sediments, 3) determining the potential risk to aquatic invertebrates, and 4) prioritizing pesticides based on their potential risk. Twelve pesticides were consistently quantified in 192 river sediments samples. The pesticides with the highest concentrations were ametrine, malathion and picloram. The temporal analysis showed seasonality in pesticide concentrations, with higher detection frequencies during the wet season. The risk assessment showed that aquatic invertebrates may be affected by the concentrations of carbofuran, malathion, diazinon and ametrine. Pesticides prioritization identified ametrine, carbofuran, and diazinon as major concerns based on the methodology that considers the Frequency and Extent of Exceedance. This study provides valuable insights into the current pesticides scenario in the Ayuquila-Armeria River sediments. The findings underscore the need for sustainable alternatives to mitigate the ecological risks associated with pesticides contamination in this aquatic ecosystem.