This study assesses the antimicrobial, antibiofilm, and antiurease properties of selenium (Se), zinc (Zn), and zinc selenide (ZnSe) nanoparticles (NPs) against clinically pathogenic strains of Streptococcus salivarius and Proteus mirabilis. The Se, Zn, and ZnSe NPs, synthesized by Pseudomonas aeruginosa OG1, were characterized using transmission electron microscopy (TEM) revealing average sizes of approximately 30 ± 10 nm, 30 ± 15 nm, and 40 ± 10 nm, respectively. Atomic force microscopy (AFM) was used to examine the morphological and topological characteristics of the NPs. The structural and crystal characteristics were investigated using X-ray diffraction (XRD). Among the evaluated NPs, Zn NPs at a concentration of 200 mg/mL exhibited the most substantial growth inhibition zone against S. salivarius. Conversely, the highest antibiofilm activity was observed against P. mirabilis, notably with 200 µg/mL Zn NPs. In the context of antiurease activity, both 100 μg Zn and ZnSe NPs caused complete urease inhibition (100%) in P. mirabilis within the initial 5 h, with notable inhibition rates of 94% and 80%, respectively, observed against S. salivarius. Significantly, in the current landscape of NP research primarily focused on antimicrobial and antibiofilm properties, our study stands out due to its pioneering exploration of antiurease activities with these NPs. This distinctive emphasis on antiurease effects contributes original and unique value to our study, offering novel insights into the broader spectrum of NP applications, and paving the way for potential therapeutic advancements.