Increased adhesion and biofilm formation by marine microalgae as well as inhibition of settlement of invertebrate larval forms on polydimethylsiloxane (PDMS) foul release coatings is a challenge to overcome. Copper oxide nanoparticles (CuO-NP) were synthesized by a wet chemical precipitation route and incorporated into PDMS foul release surfaces to improve its anti-microfouling nature. In situ antifouling performance of PDMS-CuO nanocomposite (NC) was evaluated in coastal waters and compared with plain PDMS surface. Adhesion and settlement of microalgae and macrofoulers and their succession were monitored for 7 and 90 days respectively. Plain PDMS surfaces were abundantly colonized by microalgae (1.3 × 103 cm−2), wherein significant (p < 0.05) reduction (1.76 × 102) was observed with PDMS-CuO NC. In addition, CuO reinforcement significantly (p < 0.05) reduced the biofouling load and surface area coverage upto 1.6 ± 0.22 Kg m−2 90 day−1 and 27.5 ± 4.5% respectively, whereas plain PDMS surfaces experienced 10.6 ± 1.5 Kg m−2 90 day−1 and 89.6 ± 7.96% respectively. Incorporation of CuO nanoparticles as nanofillers into PDMS matrix offers a promising antifouling alternative to inhibit algal fouling as well as larval settlement by imparting toxicity at the surface through release of metal ions.