There is an increasing interest in organic horticulture in Puerto Rico. One of the main limitations for organic production is the scarcity of local research for production recommendations. Research was conducted to evaluate mulching for weed suppression and alternative pesticides for disease management in an organic watermelon system in Lajas, Puerto Rico. Plots were either not mulched or mulched with freshly-cut grass straw. The alternative pesticides were (1) a blend of oils of rosemary, clove, thyme and wintergreen, mixed with lecithin and buthyl lactate (Sporan®), (2) hydrogen dioxide (OxiDate®), (3) an oil extract from the tea tree Melaleuca alternifolia) (Timorex®), (4) a clarified Hydrophobic Extract of neem (Azadirachta indica) oil (Trilogy®), (5) mint and rosemary oils mixed with wintergreen oil, vanillin, lecithin and buthyl lactate (Ecotrol®), (6) potassium bicarbonate (Milstop®), (7) Bacillus pumilis strain QST 2808 (Sonata®), (8) B. subtilis strain QST 713 (Serenade®), (9) whole milk (10% solution in water), (10) a garlic (Allium sativum) extract (Garlic Barrier®), (11) (Javelin®) mixed with a copper fungicide (NuCop®) alternated with B. thuringiensis (Agree®) mixed with a copper fungicide (NuCop®), and (12) a check treated with water. The organic pesticides were applied weekly at recommended rates. Downy mildew was the prevalent disease throughout the season. Watermelon yield was significantly higher in mulched plots than in non-mulched plots, due to weed suppression by the mulch. Among the organic pesticide treatments resulting in the highest crop yields were hydrogen dioxide, Bacillus pumilis strain QST 2808, the garlic extract, and the Melaleuca alternifolia oil extract. These results provide valuable information for weed and disease management in organic and ecological watermelon systems in tropical regions.