Hi,
You are performing the correct method to measure water level using pressure sensor by using the silicon tube and the column of air avoiding the sensor to be in direct contact with the water.
Sources of offset errors and drift are due to device to device offset variation (trim errors), mechanical stresses (mounting stresses), shifts due to temperature and aging. Performing auto-zero will greatly reduce these error.
Auto-zero is a compensation technique based on sampling the offset of the sensor at reference pressure in order to correct the sensor output drift or variation, this technique will correct the error on zero pressure and across the complete pressure range.
Details about the autozero technique can be found in the Application note AN1636: https://www.nxp.com/docs/en/application-note/AN1636.pdf
Regards,
Jose
NXP Semiconductors