It sounds like you have a drainage problem. All that stagnate water isn't good as it breeds bacteria. If this is a one-off event, something that just happened because there was more rain than normal for the area, then you can solve things yourself by directing the water through swales and hills. If it's a problem that occurs frequently, then you might need a professional to regrade the land. I'd try fixing it myself first though. Start redirecting that water so your muddy spots can dry up, then work on fixing the soil.