During the olive oil extraction season, a huge amount of olive mill wastewater (OMW) is produced in a short period. The uncontrolled disposal of this liquid by-product into water bodies poses significant environmental challenges in Morocco, due to its complex compositions and low biodegradability. This study evaluates the long-term effects of OMW disposal on the physicochemical properties of the wastewater treatment plant by a natural lagoon (WWTP-NL) in Zaouit Cheikh City in central Morocco. The OMW’s effect was investigated based on physicochemical analysis data of raw and treated wastewater conducted monthly over eight years. To reach this aim, two wastewater quality indices (WWQI) namely, the Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI), and the Weighted Arithmetic Water Quality Index (WA-WQI), were applied to summarize large amounts of data into a single numerical value, that is easily manageable for environmental managers. The proposed indices highlight the persistent effects of OMW on the physicochemical properties before, during, and after the harvesting season, by evaluating the effluent’s compliance with Moroccan standards for domestic discharge. According to the statistical analysis, and the WWQI scale classification, the CCME-WQI values for raw influent were 47.49 (marginal quality) before, 30.51 (poor quality) during, and 46.24 (marginal quality) after the olive harvesting season (OHS). For treated effluent, the CCME-WQI values were 55.66 (marginal quality) before, 33.61 (poor quality) during, and 55.94 (marginal quality) after OHS. For the WA-WQI, the calculated rates for raw influent range from 98.13 (bad quality), 104.60 (very bad quality), and 98.66 (bad quality) before, during, and after OHS. For treated effluent, the WA-WQI ranged from 91.58 before, 93.47 during, and 88.30 after OHS, consistently indicating bad quality across all three periods. The findings of this research indicate significant seasonal variations during OHS, marked by increased BOD5, COD, and TSS, along with decreased pH, DO, and biodegradability, with a considerable persistence of OMW pollutants after OHS compared to their levels before OHS, as confirmed by the WWQI classification. This study shows that the CCME-WQI and WA-WQI methods are effective tools for evaluating the long-term effects of OMW disposal on the WWTP-NL and providing useful information to optimize wastewater management.