Population monitoring is an essential component of biodiversity conservation and management, but low detection probabilities for rare and/or cryptic species makes estimating abundance and occupancy challenging. Passive acoustic monitoring combined with machine learning algorithms represents a potential path forward to effectively and efficiently monitor the occurrence of rare vocalizing species across entire forest landscapes. Our objectives were to develop and implement a convolutional neural network (PNW-Cnet) to identify vocalizations of a rare and threatened forest nesting bird species – the marbled murrelet (Brachyramphus marmoratus) – in the Pacific Northwest, U.S.A., 2018–2021. We used PNW-Cnet predictions from broadscale passive acoustic monitoring data to examine spatiotemporal patterns in the distribution of murrelets. PNW-Cnet showed sufficiently high prediction accuracy (overall precision > 0.9) to enable broadscale population monitoring. Spatiotemporal analysis showed that annual peak murrelet call abundance occurs in ordinal weeks 28–32 (late July–Mid August) but this varied by study area. The greatest number of detections typically occurred in the Olympic Peninsula and Oregon Coast Range where late-successional forest dominates and nearer to ocean habitats. We demonstrate that passive acoustic monitoring can be used to understand intensity of use across broad scales for a rare and cryptic species in addition to the typical detection/non-detection data that are often collected. Passive acoustic monitoring combined with PNW-Cnet offers considerable promise for species distribution modeling and long-term population monitoring for rare species.