1. Urea accounts for half of global agricultural fertiliser applications, yet little is known of its role in eutrophication of freshwater ecosystems, nor how it interacts with phosphorus (P) in regulating phytoplankton composition, especially during spring and autumn. 2. To identify when and how urea and P inputs interact across the ice‐free period, we conducted seven monthly fertilisation experiments in 3,240‐L mesocosms from ice‐off to ice‐formation in a hypereutrophic lake. In addition, we ran bioassays with ammonium (NH4+) to compare the effects of urea with those of NH4+, the immediate product of chemical decomposition of urea. 3. Analysis of water‐column chlorophyll a and biomarker pigments by high‐performance liquid chromatography revealed that addition of inorganic P alone (100 µg P L–1 week–1) had no significant impact on either algal abundance or community composition in hypereutrophic Wascana Lake. Instead, fertilisation with urea (4 mg N L−1 week–1) alone, or in concert with P, significantly (p < 0.05) increased algal abundance in spring and much of summer, but not prior to ice formation in October. In particular, urea amendment enhanced abundance of cryptophytes, chlorophytes, and non‐diazotrophic cyanobacteria during April and May, while fertilisation in summer and early autumn (September) increased only chlorophytes and non‐diazotrophic cyanobacteria. 4. Comparison of urea mesocosms with NH4+ bioassays demonstrated that urea lacked the inherent toxicity of NH4+ in cool waters, but that both compounds stimulated production during summer experiments. 5. This study showed that urea pollution can degrade water quality in P‐rich lakes across a variety of seasonal conditions, including spring, and underscores the importance of quantifying the timing and form of N inputs when managing P‐rich freshwaters.