Inland water management is increasingly important under climate change due to the need for landscape-scale water retention, but in situ studies are limited by fluctuating, shallow, and intermittent water cover. This study simulated prolonged waterlogging under controlled laboratory conditions. Four agricultural soils (Calcisol, Arenosol, Chernozem, and Solonetz) were flooded for 40 days using identical 1:5 soil-to-water ratios at two temperature regimes, at 4 and 22 °C. Given that periodic water cover may conflict with agricultural production, particular attention was paid to crop-relevant indicators, including pH, water-soluble salts, and N, P, K. The laboratory simulation revealed significant differences among soil types and between temperature treatments. Elevated Mg concentrations limited the irrigation suitability of leachate derived from Calcisol, with Mg% values ranging from 57 to 64%, exceeding the 50% guideline threshold. Soil buffering capacity controlled phosphorus and potassium dynamics, resulting in stable or slightly increasing AL-soluble nutrient levels, except in low-buffering sandy soils where up to 3–4-fold variability was observed. Reductive conditions developed early in the Calcisol samples, supported by dissolved oxygen saturation values below 20% during the first days of the experiment. Oxygen saturation increased later, only exceeding 60% twice in the cooled Calcisol treatment, while nitrate–ammonium dynamics reflected changing redox conditions. Temperature significantly affected solubility and nutrient mobility, partly through its influence on microbial activity. These findings improve our understanding of inland water–soil interactions and support the development of sustainable, water-retentive land management strategies.