Organotin compounds (OTs) are well studied in various environmental compartments, with a critical focus on the water column as their primary entry point into aquatic ecosystems. In this context, a method for the analysis of organotin (OTs) in water using silicone rubber-based passive sampling was optimized, validated, and field-tested. Validation covered crucial parameters, including the limit of detection (LOD), limit of quantification (LOQ), accuracy, precision, linearity, and matrix effect. The method was shown to be robust (R2 ≥ 0.99), with recoveries between 70.2 and 114.6%, and precise (CV < 12.8%) (N = 3). LODCw and LOQCw were ≤15 and ≤ 48 pg Sn L−1, respectively, for TBT and TPhT. The matrix effect showed to be low (>-20% ME < 20%) for all OTs but TPhT (69.4%). The silicone rubber–water partition coefficients (Log Ksr,w) were estimated at 3.37 for MBT, 3.77 for DBT, 4.17 for TBT, 3.49 for MPhT, 3.83 for DPhT, and 4.22 for TPhT. During the field study carried out between October 2021 and February 2022 at the entrance of the Port of Santos navigation channel (Southeastern Brazil), sampling rates ranged between 4.1 and 4.6 L d−1, and the equilibrium was achieved for MBT, DBT, MPhT, and DPhT after ∼45 days of deployment. The freely dissolved concentrations varied between 134 and 165 pg Sn L−1 for TBT, 388 and 610 pg Sn L−1 for DBT, and 1114 and 1509 pg Sn L−1 for MBT, while MPhT, DPhT, and TPhT were below the limit of detection. Results pointed out that J-FLEX® rubber-based passive sampling is a suitable and reliable alternative method for the continuous monitoring of OTs in the water column.