(4Z,8Z)-Matricaria lactone (MAT) and (4Z)-lachnophyllum lactone (LAC) are natural acetylenic furanones with bioherbicidal potential. This study evaluates their possibilities and ecotoxicological impact on aquatic (Aliivibrio fischeri, Raphidocelis subcapitata, and Daphnia magna) and terrestrial (Caenorhabditis elegans, Lepidum sativum) model organisms. MAT exhibited rapid degradation, with 90% decomposition within 24 h and over 98% by day 16, while LAC was more stable, degrading by only 8.5% in 24 h and 67% by day 16. Despite its rapid breakdown, MAT exhibited higher acute toxicity to A. fischeri (EC10 = 0.063 mg L−1; EC50 = 0.642 mg L−1) compared to LAC (EC10 = 0.524 mg L−1; EC50 = 8.078 mg L−1). Toxicity patterns in R. subcapitata differed, with MAT promoting slightly higher growth compared to the control, suggesting hormetic effects (EC10 = 3.417 mg L−1; EC50 = 4.520 mg L−1), while LAC inhibited growth concentration (EC10 = 0.304 mg L−1; EC50 = 9.880 mg L−1). Both compounds immobilized D. magna, with LAC showing greater delayed toxicity (EC50 = 1.728 mg L−1 vs. MAT EC50 = 2.239 mg L−1). Furthermore, for L. sativum, there were no effects on the germination, but effects were observed in the lengths of the shoots (LAC EC50 = 85.89 mg L−1 vs. MAT EC50 = 82.30 mg L−1). In contrast, C. elegans showed no mortality, suggesting lower terrestrial toxicity. These findings suggest that MAT and LAC may pose risks to aquatic ecosystems through runoff or leaching, necessitating further studies on their degradation products, soil microbiota, and non-target terrestrial organisms. Comparative analyses with conventional herbicides highlight MAT and LAC as selective, lower-impact alternatives. Future research should focus on their effects on terrestrial organisms, the ecological safety of degradation products, and large-scale bioassays to ensure their sustainability in agriculture.