The production of pearl millet (Pennisetum glaucum (L.) R.Br.) is important in Namibia, in sub-Saharan Africa, owing to the prevailing low precipitation conditions. Most fields supporting crop production in northern Namibia are located in a network of seasonal wetlands. The aim of the present study was to evaluate the effects of ridging and fertilizer application on the yield and the growth of pearl millet in the seasonal wetlands under different rainfall conditions. The study was conducted for two years (2017–2018) in the experimental fields in northern Namibia, and yield, yield components, and growth parameters were evaluated in relation to the application of different fertilizers (manure and mineral) with and without ridge-furrows. Manure fertilizer application presented the highest yield in 2018, whereas mineral fertilizer application showed the highest yield in 2017. The proportion of rainfall was the highest during the mid-growth period in 2017, and the reproductive stage in 2018. Thus, pearl millet plants under manure fertilization overcame damage resulting from waterlogging stress during the seed setting stage by improving the soil and plant nutrient conditions. In contrast, the plants under mineral fertilization were more tolerant to large amounts of rain during the mid-growth period. In this study, yield was mainly determined by total dry weight, and it was closely related to panicle density in both years. Therefore, we concluded that fertilizer application, including additional fertilizer based on the growth diagnostic, could be important for improving crop production in seasonal wetlands.