You could use the usual substitution. I use ArcTan[y,x] rather than ArcTan[y/x] because it accounts for the quadrant.
* Below edited to correct error *
In[1]:= fromPolarRule = {r -> Sqrt[x^2 + y^2], \[Theta] ->
ArcTan[x,y]};
In[2]:= eq = r Cos[\[Theta]] == r Sin[\[Theta]];
In[3]:= eqxy = eq /. fromPolarRule
Out[3]= x == y