Realistic recordings of soundscapes often have multiple sound events co-occurring, such as car horns, engine and human voices. Sound event retrieval is a type of content-based search aiming at finding audio samples, similar to an audio query based on their acoustic or semantic content. State of the art sound event retrieval models have focused on single-label audio recordings, with only one sound event occurring, rather than on multi-label audio recordings (i.e., multiple sound events occur in one recording). To address this latter problem, we propose different Deep Learning architectures with a Siamese-structure and a Pairwise Presence Matrix. The networks are trained and evaluated using the SONYC-UST dataset containing both single- and multi-label soundscape recordings. The performance results show the effectiveness of our proposed model.