Let q=pn be an odd prime power and let Fq be the finite field with q elements. Let Fq× be the group of all multiplicative characters of Fq and let χ be a generator of Fq×. In this paper, we investigate arithmetic properties of certain cyclotomic matrices involving nonzero squares over Fq. For example, let s1,s2,⋯,s(q−1)/2 be all nonzero squares over Fq. For any integer 1≤r≤q−2, define the matrix Bq,2(χr):=[χr(si+sj)+χr(si−sj)]1≤i,j≤(q−1)/2. We prove that if q≡3(mod4), then det(Bq,2(χr))=0≤k≤(q−3)/2∏Jq(χr,χ2k)={(−1)4q−3inGq(χr)2q−1/qGq(χr)2q−1/q\mboxifr≡1(mod2),\mboxifr≡0(mod2), where Jq(χr,χ2k) and Gq(χr) are the Jacobi sum and the Gauss sum over Fq respectively.