Understanding the diagenetic processes of organic matter (OM) within mangrove forests is essential to grasp ecosystem dynamics and exchanges with adjacent ecosystems. This study investigated the influence of urban runoff on leaf litter degradation in a New Caledonian mangrove forest, subjected to urban rainwater for over 50 years. Focusing on Avicennia marina and Rhizophora stylosa, our objectives were to determine factors affecting leaf litter degradation, assess urban runoff effects on decay rates and element concentrations, and understand OM changes at the molecular level. Litterbags containing senescent leaves placed on the mangrove floor were collected after 7, 14, 28, 56, and 72 days. C and N along with their stable isotopes were evaluated during degradation as well as lignin and neutral carbohydrates contents. Despite lower initial N content, R. stylosa exhibited faster degradation (t1/2 of 36 ± 3 and 28 ± 2 days) than A. marina (t1/2 of 43 ± 9 and 33 ± 4 days), emphasizing the critical role of species position within the mangrove forest regarding tidal immersion. Urban runoff, submerging the urban site, intensified leaf litter degradation, influencing both mass loss and molecular changes in OM. After 72 days of leaf litter degradation, the loss of rhamnose and glucose was more pronounced at the control site (13 % and 75 % for rhamnose and 46 % and 53 % for glucose for A. marina and R. stylosa, respectively) compared to the urban site. The study also exposed molecular tendencies during mangrove leaf litter degradation. The content of ferulic acid in the leaf litter decreased at all stands after 72 days of degradation (between −25 % and −58 %), while total syringyl phenols increased (between + 64 % and + 232 %). This research exposed the global implications of urban runoff, indicating accelerated leaf litter degradation in mangrove forests, potentially disrupting C sequestration dynamics and threatening ecosystem services.