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Pollution by agricultural pesticides is one of the most important pressures affecting Mediterranean coastal wetlands. Pesticide risks are expected to be influenced by climate change, which will result in an increase of temperatures and a decrease in annual precipitation rates in this region. On the other hand, pesticide dosages are expected to change given the increase in pest resistance and the implementation of environmental policies like the European Farm-to-Fork strategy, which aims for a 50% reduction in pesticide usage by 2030. The influence of climate change and pesticide use practices on the ecological risks of pesticides needs to be evaluated making use of realistic environmental scenarios. This study aimed to assess how different climate change and pesticide use practices affect the ecological risks of pesticides in the Albufera Natural Park (Valencia, Spain), a protected Mediterranean coastal wetland. We performed a probabilistic risk assessment for nine pesticides applied in rice production using scenarios comprised of three climatic regimes (the 2008 record, and projections for 2050 and 2100), three pesticide application regimes (the recommended dose, and 50% increase and 50% decrease), and their combinations. The scenarios were used to simulate pesticide exposure concentrations in the water column of the rice paddies using the RICEWQ model. Pesticide effects were characterized using acute and chronic Species Sensitivity Distributions built with laboratory toxicity data for aquatic organisms. Risk quotients were calculated as probability distributions making use of a Bayesian network approach, and best fitting distributions for the calculated exposure data and the SSDs. Our results show that future climate projections will influence exposure concentrations for some of the studied pesticides, yielding higher dissipation and lower exposure in scenarios dominated by an increase of temperatures, and higher exposure for scenarios in which heavy precipitation events occur after pesticide application. Our case study shows that pesticides such as azoxystrobin, difenoconazole and MCPA are posing high ecological risks for aquatic organisms, and that the implementation of the Farm-to-Fork strategy is crucial to reduce them, although will need additional measures to eliminate them.