When the PDD (percentage depth dose) in the megavoltage beams is measured in the water phantom, the polarity and ion recombination effects of ionization chambers with depth in water are not usually taken into consideration. We try to investigate if those variations with depth should be taken into consideration or could be ignored for the thimble type semiflex ionization chamber (PTW $31010^{TM}$, SN 1551). According to the recommendation of IAEA TRS-398, the 4 representative depths of $d_s$, $d_{max}$, $d_{90}$ and $d_{50}$ were used for the electron beams. For the photon beams, the 4 depths were arbitrarily chosen for the photon beams, which were $d_s$, $d_{max}$, $d_{10}$ and $d_{20}$. For the high energy photon beam both polarity and ion recombination factors of the chamber with depth in water gives the good agreements within the maximum $pm$0.2%, while the $C_{polS}$ with depth came within the maximum $pm$ 0.4% and the $C_{IRS}$ within the maximum $pm$0.6% in every electron beam used. This study shows that PDI (percentage depth ionization) could be a good approximation to PDD for the chamber used.