Passive Acoustic Monitoring is a key tool for biodiversity conservation, but the large volumes of unsupervised audio it generates present major challenges for extracting meaningful information. Deep Learning offers promising solutions. BirdNET, a widely used bird identification model, has shown success in many study systems but is limited at local scale due to biases in its training data, which focus on specific locations and target sounds rather than entire soundscapes. A key challenge in bird species identification is that many recordings either lack target species or contain overlapping vocalizations, complicating automatic identification. To address these problems, we developed a multi-stage pipeline for automatic bird vocalization identification in Doñana National Park (SW Spain), a wetland of high conservation concern. We deployed AudioMoth recorders in three main habitats across nine locations and manually annotated 461 minutes of audio, resulting in 3749 labeled segments spanning 34 classes. We first applied a Bird Song Detector to isolate bird vocalizations using spectrogram-based image processing. Then, species were classified using custom models trained at the local scale. Applying the Bird Song Detector before classification improved species identification, as all models performed better when analyzing only the segments where birds were detected. Specifically, the combination of detector and fine-tuned BirdNET outperformed the baseline without detection. This approach demonstrates the effectiveness of integrating a Bird Song Detector with local classification models. These findings highlight the need to adapt general-purpose tools to specific ecological challenges. Automatically detecting bird species helps track the health of this threatened ecosystem, given birds sensitivity to environmental change, and supports conservation planning to reduce biodiversity loss.