Generally, women residing in areas endemic for urinary schistosomiasis may suffer from female genital schistosomiasis which is acquired during childhood. The objective of this cross-sectional study was to estimate the prevalence and intensity of infection of Schistosoma haematobium in women of reproductive age (16–45 years) and to investigate whether S. haematobium had any effect on kidney function. A total of 394 women of known pregnancy status (158 pregnant and 236 non-pregnant) were recruited from five villages (known for their high prevalence of infection of S. haematobium) in Kwale County. Serum samples were analysed to determine levels of urea and creatinine as proxy indicators of kidney function. Data revealed that pregnant women did not, on average, have a higher prevalence or intensity of infection of urinary schistosomiasis than non-pregnant women. During pregnancy, the level of prevalence and intensity of infection of S. haematobium was highest in the first trimester (0–13 weeks), dropped in the second trimester (14–26 weeks) and rose again in the third trimester (27–40 weeks). In addition, 24.8% of women were infected with hookworm, while none were diagnosed with malaria parasites. Of 250 samples analysed for serum urea and creatinine, none had significant levels of pathology, either in pregnant or non-pregnant women. Despite World Health Organization (WHO) recommendations that pregnant women should be treated with praziquantel after the first trimester, in practice this has not been the case in many countries, including Kenya. In view of this, healthcare providers should be informed to consider treatment of pregnant women infected with schistosomiasis during antenatal visits and whenever there is mass drug administration as recommended by the WHO.