The treatment of bacterial diseases in aquaculture is done using antibiotics, their applications has resulted in contamination and bacterial resistance. Natural extracts are a potential alternative as an antimicrobial, they have demonstrated effectiveness in their use aimed at treating conditions. The purpose of this study was to evaluate the antimicrobial activity of
Lemna minor
extracts against
Pseudomonas fluorescens
with different solvent for extraction. Methanol, chloroform and hexane were used. Subsequently, the safety assessment of the extracts in
Danio rerio
embryos and larvae was performed to validate as ecologically harmless. Antibacterial activity was detected in three extracts with significant differences (p = 0.001). Hexane extract had the highest antibacterial activity, followed by chloroform and methanol extracts. The three extracts have differences with respect to the control, between times and concentrations tested (p = 0.001). Minimum inhibitory concentration values (MIC) at 24 h methanolic extract ME 0.05 µg mL
−1
. In embryos and larvae increased safety of the LC
50
methanolic extract was evidenced followed by the hexane and chloroform extract. No morphological or tissue changes were observed in embryos and larvae. The hexane extracts of
L. minor
had a greater bactericidal effect against
P. fluorescens
and are functional because of their antibacterial activity, but methanolic extract is more safety in embryos and larvae of
D. rerio
, making it a potential alternative for use in the treatment and control of septicemia in fish.