The bioactive sulfated polysaccharide from brown algae, fucoidan, can be used for a wide array of applications. As with other natural products, there are seasonal variabilities as well as variability within the investigated species, across regions, and from using different extraction procedures. In this study, the use of hot demineralized water and two variations of hot acidified water (10 mM sulfuric acid and 100 mM hydrochloric acid) as extraction solvents for microwave extraction of fucoidan from three different brown algae of the Fucus genus (F. vesiculosus, F. serratus, and F. evanescens) were investigated. The effect on yield of fucoidan from the different solvents at temperatures 80 °C, 100 °C, 120 °C was tested. The Fucus used in this study were harvested in the Baltic Sea in the Kiel Fjord, Germany, during Summer and Autumn of 2017. Air dried F. vesiculosus from Brittany in France was also analyzed and used for optimization of the extraction method and as a reference sample. The extraction procedure was adapted and modified from the method provided by Fletcher et al. (2017). The extracts were purified by performing dialysis. The results showed that fucoidan yield is maximized by extracting with 10 mM sulfuric acid for all species investigated. A large seasonal variance between species was observed, and large differences in yield were also dependent on species. These results suggest that to maximize fucoidan yield, one should tailor the extraction method to the specific algae species used, however, microwave assisted extraction (MAE) with 10 mM sulfuric acid proves a good general extraction method.