Best known deterministic time complexity lower bound for a natural problem in NP
Adachi, Iwata, and Kasai in a 1984 JACM paper show by reduction that the Cat and $k$-Mice game has an $n^{\Omega(k)}$ time lower bound.   The problem is in P for each $k$.   The problem is played on a directed graph.    The moves consist of the cat and then one of the $k$ mice alternating steps.  The mice win if they can land on a designated cheese node before the cat lands on them.   The question is whether the cat has a forced win.   It is actually a complete problem so the lower bound is really based on the diagonalization that gives the time hierarchy. 

Grandjean showed that the Pippenger, Paul, Szemeredi, and Trotter time lower bound applies to a SAT encoding, though the result of Santhanam may subsume it.

In addition to the time-space tradeoff lower bounds for SAT mentioned in other comments, there is a body of work on branching program lower bounds which imply time-space tradeoffs for Turing machines.    For problems like FFT, sorting or computing universal hash functions there are quadratic tradeoff lower bounds of Borodin-Cook, Abrahamson, Mansour-Nisan-Tiwari but these are for functions with many outputs.   For decision problems in P, there are time-space tradeoff lower bounds that apply for time bounds that are $O(n \log n)$ but these are weaker than are known for SAT.