Uncertainties about the magnitude of bycatch in poorly assessed fisheries impede effective conservation management. In northern Peru, small-scale fisheries (SSF) bycatch negatively impacts marine megafauna populations and the livelihoods of fishers which is further elevated by the under-reporting of incidents. Within the last decade, accounts of entangled humpback whales (HBW) (Megaptera novaeangliae) off the northern coast of Peru have increased, while Eastern Pacific leatherback turtles (LBT) (Dermochelys coriacea) have seen over a 90% decline in nesting populations related in large part to bycatch mortality. By leveraging the experience and knowledge of local fishers, our research objectives were to use a low-cost public participation mapping approach to provide a spatio-temporal assessment of bycatch risk for HBW and LBT off two Peruvian fishing ports. We used an open-source, geographic information systems (GIS) model, the Bycatch Risk Assessment (ByRA), as our platform. Broadly, ByRA identifies high bycatch risk areas by estimating the intersection of fishing areas (i.e., stressors) with species habitat and evaluating the exposure and consequence of possible interaction between the two. ByRA outputs provided risk maps and gear risk percentages categorized as high, medium, and low for the study area and seven subzones for HBW in the austral winter and LBT in the austral summer. Overall, the highest bycatch risk for both species was identified within gillnet fisheries near the coast. Bycatch risk for most gear types decreased with distance from the coast. When we separated the ByRA model by port, our map outputs indicate that bycatch management should be port specific, following seasonal and spatial variations for HBW, and specific fishing gear impacts for HBW and LBT. Combined with direct bycatch mitigation techniques, ByRA can be a supportive and informative tool for addressing specific bycatch threats and marine megafauna conservation goals. ByRA supports a participatory framework offering rapid visual information via risk maps and replicable methods for areas with limited resources and data on fisheries and species habitat.