Although snake populations are suffering numerous local declines, determining the scale of these declines is problematic due to the elusive nature of snakes. Determining the factors associated with species detection is therefore essential for quantifying disturbance effects on populations. From 2017 to 2019, we assessed the detectability associations of five river-associated snake species and all snake detections in general within two logging concessions in Sabah, Malaysian Borneo. Data collected from both stream transects and visual encounter surveys at 47 stream sites were incorporated into an occupancy-modelling framework to determine the climatological, temporal and survey distance associations with species detection probability. Detection probability of riparian snake species was significantly associated with humidity, month (2 spp. each), survey distance and total rainfall over 60 days (1 spp. each). Pooled snake species detectability was significantly positively associated with transect distance and the 2019 El-Niño year, whilst yearly pooled snake species detections in stream transects spiked during El-Niño (2017 = 2.05, 2018 = 2.47, 2019 = 4.5 snakes per km). This study provides new insights into the detectability of riparian rainforest snakes and suggests that future studies should account for short-term (climatological and temporal) and long-term (El-Niño) factors associated with detection probability when surveying and assessing snake populations.