Crete faces increasing water scarcity driven by climate change, tourism, and intensive agriculture, leading to a growing reliance on alternative water sources - including treated wastewater - for irrigation. While this approach supports water conservation, it raises critical toxicological and environmental concerns. Our laboratory plays a key role in the routine monitoring and quality control of both conventional and reclaimed water used for agricultural irrigation across the island. This study presents findings from multi-year surveillance programs evaluating the chemical, microbiological, and emerging contaminant profiles of irrigation water sources in Crete. Particular attention is given to the detection of nutrients, heavy metals, and microbial indicators in treated effluents considered for reuse. Data trends reveal seasonal and regional variability, and in some cases, exceedances of regulatory thresholds, underscoring the need for stricter controls and the application of advanced treatment processes. We highlight the importance of robust, ISO-accredited laboratory practices in supporting safe wastewater reuse and preventing long-term soil contamination, crop uptake of toxicants, and potential health risks. Our work also emphasizes the need for greater integration of private laboratories in regional water management strategies, farmer education, and real-time risk assessment.