Acid buildup in muscle tissue. Here is an article that explains what is happening:

https://www.pfizer.com/news/articles/science_fact_or_science_fiction_lactic_acid_buildup_causes_muscle_fatigue_and_soreness

Esit: I originally said that your.muscles are creating waste chemicals quicker than your bloodstream can handle causing those bad chemicals build up locally. While this is true in a broader sense, I think it is more nuanced that that. Reading the article should give a better explaination