The freshwater tucuxi (Sotalia flluviatilis) and the Amazon River dolphin (Inia geoffrensis) are endemic to the Amazon-Orinoco river basin. Their conservation is hindered by human disturbance and uncertainty about total population size and distribution. In this study, we used rapid assessment questionnaires to identify threats to river dolphins in Peru and to identify priority areas for their further study and conservation. We administered questionnaires to fishers (surveyed 2010 n = 162, 2015 n = 251) and community members (surveyed 2015 only; n = 118) at 12 landing ports of the Peruvian Amazon, asking questions about their knowledge, perception and interactions with river dolphins. Dolphins were observed by interviewed fishers based across all ports except for Aguaytia port, which was subsequently excluded from further analysis. Across the sampled ports in 2010, an average of 86 % of fishers (range: 59–100%; n = 8 ports) associated dolphins with negative economic impacts, largely due to net damage with similar findings in the more extensive survey in 2015 (74%, 27–100%; n = 11 ports). Bycatch of dolphins was also reported in 11 ports, with a higher incidence in the Loreto, where up to 10 bycaught individuals per fisher per year were reported for both time periods. The use of dolphins as bait has been practised from at least 2010 (2010: 31% of fishers, 11–57%; 2015: 31%, 0–63%) and is prevalent (>40%) in four of the surveyed ports (Caballococha, Bagazan, Requena and Manantay). Our study can be used as a first reference to guide monitoring of river dolphin populations in priority areas. Future efforts should revisit and extend this survey to other ports in Peru. Doing so will enable detection of trends in fisheries conflicts with river dolphins and improve the estimation of bycatch and direct take of dolphins in the Peruvian Amazon.