Why can't the EC and the PH sensors be on at the same time?
If they really can't then either the Arduino checks their values in turn an saves the results for sending to the RPi in the next message or the RPi can send a message to the Arduino telling it what to do next. This is really a matter of system design rather than writing code.
Have a look at the examples in Serial Input Basics - simple reliable ways to receive data.
The technique in the 3rd example will be the most reliable.
You can send data in a compatible format with code like this
Serial.print('<'); // start marker
Serial.print(value1);
Serial.print(','); // comma separator
Serial.print(value2);
Serial.println('>'); // end marker
All of this concept can be used in any programming language so it is as valid for receiving the data on the RPi as on the Nano.
This Python - Arduino demo may also be of interest.
...R